Statistical and Machine Learning Approaches for Network Analysis

MATTHIAS DEHMER, PHD, is Head of the Institute for Bioinformatics and Trans- lational Research at the University for Health Sciences, Medical Informatics and Technology (Austria). He has written over 130 publications in his research areas, which include bioinformatics, systems biology, and applied discrete mathematics. Dr. Dehmer is also the coeditor of Applied Statistics for Network Biology, Statistical Modelling of Molecular Descriptors in QSAR/QSPR, Medical Biostatistics for Complex Diseases, Analysis of Complex Networks, and Analysis of Microarray Data, all published by Wiley. SUBHASH C. BASAK, PHD, is Senior Research Associate at the Natural Resources Research Institute. He has published extensively in the areas of biochemical pharmacology, toxicology, mathematical chemistry, and computational chemistry.

• Preface ixContributors xi1 A Survey of Computational Approaches to Reconstruct and Partition Biological Networks 1Lipi Acharya, Thair Judeh, and Dongxiao Zhu2 Introduction to Complex Networks: Measures, Statistical Properties, and Models 45Kazuhiro Takemoto and Chikoo Oosawa3 Modeling for Evolving Biological Networks 77Kazuhiro Takemoto and Chikoo Oosawa4 Modularity Configurations in Biological Networks with Embedded Dynamics 109Enrico Capobianco, Antonella Travaglione, and Elisabetta Marras5 Influence of Statistical Estimators on the Large-Scale Causal Inference of Regulatory Networks 131Ricardo de Matos Simoes and Frank Emmert-Streib6 Weighted Spectral Distribution: A Metric for Structural Analysis of Networks 153Damien Fay, Hamed Haddadi, Andrew W. Moore, Richard Mortier, Andrew G. Thomason, and Steve Uhlig7 The Structure of an Evolving Random Bipartite Graph 191Reinhard Kutzelnigg8 Graph Kernels 217Matthias Rupp9 Network-Based Information Synergy Analysis for Alzheimer Disease 245Xuewei Wang, Hirosha Geekiyanage, and Christina Chan10 Density-Based Set Enumeration in Structured Data 261Elisabeth Georgii and Koji Tsuda11 Hyponym Extraction Employing a Weighted Graph Kernel 303Tim vor der Br¨uckIndex 327